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Data collections can be seen on:

http://researchdata.ands.org.au/breast-cancer-tissue-bank

Instruments where data are captured/transferred from:

digital imaging microscopic slide scanner: Hamamatsu Nanozoomer

Software is available at:

http://code.google.com/p/ndpi-splitter/

Project Members:

Jane Carpenter (Australian Breast Cancer Tissue Bank Contact, Jane.Carpenter@sydney.edu.au)

ANDS Contact:

Ingrid Mason (Ingrid.Mason@ands.org.au)

Project Status:

Completed

Management, Re-Use and Discovery of Breast Cancer Microscopy Virtual Images

University of Sydney

Project Description:

Software was constructed in this project to allow wide use and re-use of microscopy images in breast cancer research, generated at the Westmead Institute for Cancer Research (WICR), in analysis and study by approved researchers across Australia. The software functions include: image splitting and empty image tile detection; sharing snapshot image files with pan and zoom via online search facility; and collection metadata describing the image collections published to Research Data Australia.

Data Type:

breast cancel tissue image

High Level Software Functionality:

Features: "WP1: Build a tool to select areas of the large .NDPI image and convert these smaller segments to formats suitable for analysis and distribution.
1. Implement a web application that allows users to browse lists and metadata for the available image files
2. Implement a search module to allow users to search for image files satisfying specified metadata conditions
3. Implement a module that allows users to navigate a
EIF017 Data Capture project proposal Page 8 of 15
low-resolution graphic of the complete image and select one or more segments to download
4. Implement a module that allows individual image segments to be ?reconstituted? or stitched together in a suitable analysis environment.

WP2: Build a web portal to allow the sharing of image files amongst approved researchers.
1. Implement a web application that allows users to browse lists and metadata for the available image files
2. Implement a search module to allow users to search for image files satisfying specified metadata conditions
3. Implement a module that allows users to navigate a
EIF017 Data Capture project proposal Page 8 of 15
low-resolution graphic of the complete image and select one or more segments to download
4. Implement a module that allows individual image segments to be ?reconstituted? or stitched together in a suitable analysis environment.

WP3: Develop an approach or tool for harvesting suitable metadata fields for inclusion in the ANDS collections registry
* Determination of the best approach will be made during analysis, in close discussion with ANDS. Possible alternatives include a crosswalk from the metadata schema chosen to RIF-CS, an OAI-PMH feed or just an XML ""blob"" fetched from a known location.";

ANZSRC-FOR code:

11 MEDICAL AND HEALTH SCIENCES